Hi, i have had this issue happen a few times, where the remote stops working after the box is sitting unused overnight. And now it seems to be happening more frequently.
I reboot the box with a hard power off (pull the plug), and it pairs up again as expected. Here is a description of a most recent problem:
When I turned the TV on this morning, it automatically restarted the show we paused at dinnertime yesterday (in Amazon). Then, when I wanted to turn that off, none of the remote buttons worked. I restarted the roku box and was able to use the remote. Watched one episode on Netflix and went to turn it off, but now the remote is not working again.
This is with fresh batteries. Purchased the Roku Ultra two weeks ago and have lost pairing at least 5 times. Remote works perfectly when it works, if that makes sense. Its either working or not, nothing in between.